[gmx-users] 4.6.3 and MKL

Szilárd Páll szilard.pall at cbr.su.se
Thu Jul 11 10:50:09 CEST 2013 

FYI: The MKL FFT has been shown to be up to 30%+ slower than FFTW 3.3.
--
Szilárd


On Thu, Jul 11, 2013 at 1:17 AM, Éric Germaneau <germaneau at zoho.com> wrote:
> I have the same feeling too but I'm not in charge of it unfortunately.
> Thank you, I appreciate.
>
>
> On 07/11/2013 07:15 AM, Mark Abraham wrote:
>>
>> No problems :-) (For the record, the fact that you had to brute-force
>> static libraries in another thread does not fill me with confidence
>> that your compiler is installed correctly. But that is for you to
>> judge! :-)
>>
>> On Thu, Jul 11, 2013 at 1:11 AM, Éric Germaneau <germaneau at zoho.com>
>> wrote:
>>>
>>> I see.
>>> Thank you.
>>>
>>>
>>> On 07/11/2013 07:08 AM, Mark Abraham wrote:
>>>>
>>>> On Thu, Jul 11, 2013 at 1:02 AM, Éric Germaneau <germaneau at zoho.com>
>>>> wrote:
>>>>>
>>>>> Yes, as one can see in my first post.
>>>>
>>>> No, because we can't guess whether your icc is 11 or not. If so, you
>>>> have a bunch of stuff that is not required. icc 11 has a magic flag
>>>> for using MKL, which GROMACS will use if given the chance. But I guess
>>>> I wasted my time implementing and documenting it :-)
>>>>
>>>>> One thing is I don't know what libraries I need and in which order.
>>>>
>>>> ... and neither does anybody else who can't see the documentation for
>>>> your system. That's why if you have icc before version 11, the GROMACS
>>>> instructions suggest you look at them! That is the price of using mkl
>>>> before icc-11.
>>>>
>>>> Mark
>>>>
>>>>> Thanks,
>>>>>
>>>>>                  Eric.
>>>>>
>>>>>
>>>>> On 07/11/2013 06:58 AM, Mark Abraham wrote:
>>>>>>
>>>>>> Are you following the advice here?
>>>>>>
>>>>>>
>>>>>> http://www.gromacs.org/Documentation/Installation_Instructions#3.4.2._MKL
>>>>>>
>>>>>> On Thu, Jul 11, 2013 at 12:24 AM, Éric Germaneau <germaneau at zoho.com>
>>>>>> wrote:
>>>>>>>
>>>>>>> Dear all,
>>>>>>>
>>>>>>> Anyone have successfully built the 4.6.3 release using MKL?
>>>>>>> I keep getting the following error message:
>>>>>>>
>>>>>>>       -- Looking for DftiCreateDescriptor - not found
>>>>>>>       CMake Error at CMakeLists.txt:1018 (message):
>>>>>>>          Linking with MKL was requested, but was not successful.  The
>>>>>>>       include path
>>>>>>>          to mkl.h in MKL_INCLUDE_DIR, and the link libraries in
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> MKL_LIBRARIES=/lustre/utility/intel/mkl/lib/intel64/libmkl_intel_thread.so;/lustre/utility/intel/mkl/lib/intel64/libmkl_core.so;/lustre/utility/intel/mkl/lib/intel64/libfftw2xf_double_intel.a;/lustre/utility/intel/mkl/lib/intel64/libmkl_avx2.so;/lustre/utility/intel/mkl/lib/intel64/libmkl_scalapack_lp64.so;/lustre/utility/intel/mkl/lib/intel64/libmkl_intel_lp64.so
>>>>>>>          need to match what the MKL documentation says you need for
>>>>>>> your
>>>>>>>       system.
>>>>>>>          Use full paths to library files, in the right order, and
>>>>>>> separated
>>>>>>> by
>>>>>>>          semicolons.
>>>>>>>
>>>>>>> Here is how I use CMAKE:
>>>>>>>
>>>>>>>       CC=mpicc CXX=mpicxx
>>>>>>>
>>>>>>> CMAKE_PREFIX_PATH=$CUDAPATH/include:$CUDAPATH/lib64:$CUDAPATH/bin
>>>>>>> \
>>>>>>>          /lustre/utility/bin/cmake \
>>>>>>>           -DGMX_FFT_LIBRARY=mkl \
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> -DMKL_LIBRARIES="${MKL}/lib/intel64/libmkl_intel_thread.so;${MKL}/lib/intel64/libmkl_core.so;${MKL}/lib/intel64/libfftw2xf_double_intel.a;${MKL}/lib/intel64/libmkl_avx2.so;${MKL}/lib/intel64/libmkl_scalapack_lp64.so;${MKL}/lib/intel64/libmkl_intel_lp64.so"
>>>>>>>       \
>>>>>>>           -DMKL_INCLUDE_DIR="${MKL}/include" \
>>>>>>>           -DGMX_MPI=ON \
>>>>>>>           -DGMX_GPU=OFF [-DCUDA_TOOLKIT_ROOT_DIR=$CUDAPATH] \
>>>>>>>           -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR \
>>>>>>>           -DGMX_X11=OFF ../$APP \
>>>>>>>           -DGMX_THREADS=OFF
>>>>>>>
>>>>>>> Any hints here?
>>>>>>> I thank you in advance,
>>>>>>>
>>>>>>>                                                  'Eric.
>>>>>>>
>>>>>>> --
>>>>>>> /Be the change you wish to see in the world
>>>>>>> / --- Mahatma Gandhi ---
>>>>>>>
>>>>>>> Éric Germaneau <http://hpc.sjtu.edu.cn/index.htm>
>>>>>>>
>>>>>>> Shanghai Jiao Tong University
>>>>>>> Network & Information Center
>>>>>>> room 205
>>>>>>> Minhang Campus
>>>>>>> 800 Dongchuan Road
>>>>>>> Shanghai 200240
>>>>>>> China
>>>>>>>
>>>>>>> View Éric Germaneau's profile on LinkedIn
>>>>>>> <http://cn.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986>
>>>>>>>
>>>>>>> /Please, if possible, don't send me MS Word or PowerPoint attachments
>>>>>>> Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/
>>>>>>>
>>>>>>> --
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>>>>>
>>>>>
>>>>> --
>>>>> /Be the change you wish to see in the world
>>>>> / --- Mahatma Gandhi ---
>>>>>
>>>>> Éric Germaneau <http://hpc.sjtu.edu.cn/index.htm>
>>>>>
>>>>> Shanghai Jiao Tong University
>>>>> Network & Information Center
>>>>> room 205
>>>>> Minhang Campus
>>>>> 800 Dongchuan Road
>>>>> Shanghai 200240
>>>>> China
>>>>>
>>>>> View Éric Germaneau's profile on LinkedIn
>>>>> <http://cn.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986>
>>>>>
>>>>> /Please, if possible, don't send me MS Word or PowerPoint attachments
>>>>> Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/
>>>>>
>>>>> --
>>>>> gmx-users mailing list    gmx-users at gromacs.org
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>>>
>>>
>>> --
>>> /Be the change you wish to see in the world
>>> / --- Mahatma Gandhi ---
>>>
>>> Éric Germaneau <http://hpc.sjtu.edu.cn/index.htm>
>>>
>>> Shanghai Jiao Tong University
>>> Network & Information Center
>>> room 205
>>> Minhang Campus
>>> 800 Dongchuan Road
>>> Shanghai 200240
>>> China
>>>
>>> View Éric Germaneau's profile on LinkedIn
>>> <http://cn.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986>
>>>
>>> /Please, if possible, don't send me MS Word or PowerPoint attachments
>>> Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/
>>>
>>> --
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>
>
> --
> /Be the change you wish to see in the world
> / --- Mahatma Gandhi ---
>
> Éric Germaneau <http://hpc.sjtu.edu.cn/index.htm>
>
> Shanghai Jiao Tong University
> Network & Information Center
> room 205
> Minhang Campus
> 800 Dongchuan Road
> Shanghai 200240
> China
>
> View Éric Germaneau's profile on LinkedIn
> <http://cn.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986>
>
> /Please, if possible, don't send me MS Word or PowerPoint attachments
> Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/
>
> --
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